My fault my own fault !

Our galaxy instance is running as a service.
I forgot to modify the export path command in the galaxy daemon config file
which we setup in the /etc/init.d directory
Shame on me


2013/6/26 Jeremy Goecks <>

> >
> > To have Trackster visualization working properly in Galaxy, one needs
> bedtools.
> > Yet in our instance (running under Ubuntu OS), installing bedtools in
> the galaxy home directory and setting the environmental variable PATH in
> the .profile file so that it includes the path to ~/bin/bedtools does not
> work.
> > Yet the PATH variable is indeed including the appropriate information as
> the owner of the galaxy home directory can run the bedtools in command
> lines.
> > I have also to precise that we use a lot of third party tools (bowtie,
> cufflinks, etc...) including wigToBigWig which is also required for
> trackster, and that we have no path problem with these tools.
> >
> > Indeed the only way to get galaxy accessing properly to the bedtools
> currently is to put the bedtools in the /usr/local/bin directory. Here it
> works !
> >
> > I suspect it is a problem of shell specification when the bedtools are
> used for trackster, but I could not figure out further the issue.
> It's difficult to speculate about what's going on.
> Trackster uses the same infrastructure (PATH, submission script, etc.) for
> running bedtools that other Galaxy tools use, so there's reason to think
> that Trackster requires something special in any way. I also have multiple
> instances where bedtools is installed alongside
> bowtie/cufflinks/tophat/wigToBigWig/etc. in a single bin directory that is
> in the Galaxy user's path, and that works for me.
> You could certainly modify the conversion tools that Trackster uses to
> echo and inspect the PATH. Let us know if you find anything interesting.
> Best,
> J.


Christophe Antoniewski

Drosophila Genetics and Epigenetics
Laboratoire de Biolologie du Développement
9, Quai St Bernard, Boîte courrier 24
75252 Paris Cedex 05

Tel +33 1 44 27 34 39
Fax +33 1 44 27 34 45
Mobile +33 6 68 60 51 50
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